Biology subjects

Ralser, M.

Publications and source records attributed to Ralser, M..

5 recordsLinked to original sources

bioRxiv2018

MTA proteins act redundantly within the NuRD complex to ensure fidelity of ES cell lineage commitment

Multiprotein chromatin remodelling complexes show remarkable conservation of function amongst metazoans, even though components present in invertebrates are often present as multiple paralogous proteins in vertebrate complexes. In some cases these paralogues specify distinct biochemical and/or functional activities in vertebrate cells. Here we set out to define the biochemical and functional diversity encoded by one such group of proteins within the mammalian Nucleosome Remodelling and Deacetylation (NuRD) complex: Mta1, Mta2 and Mta3. We find that, in contrast to what has been described in somatic cells, MTA proteins are not mutually exclusive within ES cell NuRD and, despite subtle differences in chromatin binding and biochemical interactions, serve largely redundant functions. Nevertheless, ES cells lacking all three MTA proteins represent a complete NuRD null and are viable, allowing us to identify a previously undetected function for NuRD in maintaining differentiation trajectory during early stages of lineage commitment.

developmental biology↗

bioRxiv2018

DIA-NN: Deep neural networks substantially improve the identification performance of Data-independent acquisition (DIA) in proteomics

Data-independent acquisition (DIA-MS) strategies, like SWATH-MS, have been developed to increase consistency, quantification precision and proteomic depth in label-free proteomic experiments. They aim to overcome stochasticity in the selection of precursor ions by utilising (mass-) windowed acquisition that is followed by computational reconstruction of the chromatograms. While DIA methods increasingly outperform typical data-dependent methods in identification consistency and precision specifically on large sample series, possibilities remain for further improvements. At present, only a fraction of the information recorded in the complex DIA spectra is extracted by the software analysis pipelines. Here we present a software tool (DIA-NN) that introduces artificial neural nets and a new quantification strategy to enhance signal processing in DIA-data. DIA-NN greatly improves identification of precursor ions and, as a consequence, protein quantification accuracy. The performance of DIA-NN demonstrates that deep learning provides opportunities to boost the analysis of data-independent acquisition workflows in proteomics.

bioinformatics↗

bioRxiv2017

A Yeast Global Genetic Screen Reveals that Metformin Induces an Iron Deficiency-Like State

We report here a simple and global strategy to map out gene functions and target pathways of drugs, toxins or other small molecules based on \"homomer dynamics\" Protein-fragment Complementation Assays (hdPCA). hdPCA measures changes in self-association (homomerization) of over 3,500 yeast proteins in yeast grown under different conditions. hdPCA complements genetic interaction measurements while eliminating confounding effects of gene ablation. We demonstrate that hdPCA accurately predicts the effects of two longevity and health-span-affecting drugs, immunosuppressant rapamycin and type II diabetes drug metformin, on cellular pathways. We also discovered an unsuspected global cellular response to metformin that resembles iron deficiency. This discovery opens a new avenue to investigate molecular mechanisms for the prevention or treatments of diabetes, cancers and other chronic diseases of aging.

systems biology↗

bioRxiv2017

A lncRNA/Lin28/Let7 Axis Coupled To DNA Methylation Fine Tunes The Dynamics Of A Cell State Transition

Execution of pluripotency requires progression from the naive status represented by mouse embryonic stem cells (ESCs) to a condition poised for lineage specification. This process is controlled at transcriptional, post-transcriptional and epigenetic levels and non-coding RNAs are contributors to this regulation complexity. Here we identify a molecular cascade initiated by a long non-coding RNA (lncRNA), Ephemeron (Epn), that modulates the dynamics of exit from naive pluripotency. Epn deletion delays the extinction of ESC identity, an effect mediated by perduring expression of the pivotal transcription factor Nanog. In the absence of Epn, Lin28a expression is reduced, resulting in an elevated level of Mirlet7g that suppresses de novo methyltransferases Dnmt3a/b. Dnmt3a/b deletion also retards exit from the ESC state, and is associated with delayed promoter methylation and slower down-regulation of Nanog. Altogether, our findings reveal a lncRNA/miRNA/DNA methylation axis that facilitates a timely stem cell state transition.

cell biology↗

bioRxiv2017

The Nucleosome Remodelling and Deacetylation complex restricts Mediator access to enhancers to control transcription

A number of different chromatin remodelling complexes in mammalian cells are implicated in the control of gene expression. The genetic requirements for many such complex components have been described, and the biochemical activities of complex components characterised in vitro, yet the molecular mechanisms by which these biochemical activities impact transcriptional regulation in vivo remain ill-defined. Using an inducible system with fine temporal resolution, we show that the Nucleosome Remodelling and Deacetylation (NuRD) complex directly regulates chromatin architecture at enhancer regions in ES cells, in turn influencing the activity of RNA polymerase II via Mediator. Through this mechanism NuRD restricts Mediator access to enhancer chromatin during lineage commitment, thereby enabling appropriate transcriptional regulation. In contrast, acetylation levels of histone H3 lysine 27 are not immediately impacted by NuRD activity, correlating with transcriptional response only after expression levels have changed. These findings provide a detailed, molecular picture of genome-wide modulation of lineage-specific transcription by an abundant chromatin remodelling complex.

molecular biology↗